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        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        About MultiQC

        This report was generated using MultiQC, version 1.9

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        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2021-04-07, 17:19 based on data in: /node/accredetation/2021/16s/Nextflow/16S_Accreditation/Nextflow/work/f7/8820e974d77379b85e14312320d787


        General Statistics

        Showing 248/248 rows and 4/5 columns.
        Sample Name% Dups% GCLengthM Seqs
        S100_R1.paired
        73.4%
        55%
        226 bp
        0.1
        S100_R2.paired
        35.7%
        54%
        187 bp
        0.1
        S101_R1.paired
        65.3%
        51%
        231 bp
        0.1
        S101_R2.paired
        40.4%
        50%
        234 bp
        0.1
        S102_R1.paired
        73.6%
        51%
        241 bp
        0.1
        S102_R2.paired
        42.6%
        50%
        239 bp
        0.1
        S103_R1.paired
        82.4%
        51%
        242 bp
        0.4
        S103_R2.paired
        58.7%
        49%
        236 bp
        0.4
        S104_R1.paired
        82.7%
        53%
        239 bp
        0.3
        S104_R2.paired
        63.0%
        52%
        235 bp
        0.3
        S105_R1.paired
        74.0%
        53%
        237 bp
        0.2
        S105_R2.paired
        45.2%
        52%
        227 bp
        0.2
        S106_R1.paired
        84.0%
        53%
        241 bp
        0.4
        S106_R2.paired
        56.0%
        52%
        229 bp
        0.4
        S107_R1.paired
        74.8%
        52%
        238 bp
        0.1
        S107_R2.paired
        51.8%
        51%
        218 bp
        0.1
        S10_R1.paired
        72.4%
        52%
        243 bp
        0.2
        S10_R2.paired
        37.0%
        51%
        228 bp
        0.2
        S110_R1.paired
        80.9%
        53%
        239 bp
        0.4
        S110_R2.paired
        66.1%
        52%
        233 bp
        0.4
        S112_R1.paired
        65.9%
        54%
        237 bp
        0.0
        S112_R2.paired
        23.5%
        52%
        226 bp
        0.0
        S113_R1.paired
        79.6%
        52%
        242 bp
        0.3
        S113_R2.paired
        50.6%
        50%
        228 bp
        0.3
        S114_R1.paired
        79.6%
        50%
        242 bp
        0.3
        S114_R2.paired
        51.0%
        49%
        236 bp
        0.3
        S115_R1.paired
        69.8%
        49%
        243 bp
        0.1
        S115_R2.paired
        31.5%
        48%
        240 bp
        0.1
        S117_R1.paired
        81.1%
        54%
        239 bp
        0.3
        S117_R2.paired
        49.1%
        53%
        233 bp
        0.3
        S119_R1.paired
        84.7%
        52%
        229 bp
        0.3
        S119_R2.paired
        69.7%
        51%
        235 bp
        0.3
        S122_R1.paired
        82.0%
        53%
        241 bp
        0.3
        S122_R2.paired
        73.1%
        51%
        236 bp
        0.3
        S123_R1.paired
        75.5%
        53%
        241 bp
        0.2
        S123_R2.paired
        48.3%
        51%
        232 bp
        0.2
        S124_R1.paired
        71.0%
        51%
        237 bp
        0.1
        S124_R2.paired
        41.2%
        50%
        234 bp
        0.1
        S125_R1.paired
        78.4%
        53%
        224 bp
        0.1
        S125_R2.paired
        56.1%
        51%
        232 bp
        0.1
        S126_R1.paired
        79.3%
        53%
        240 bp
        0.4
        S126_R2.paired
        48.4%
        51%
        226 bp
        0.4
        S127_R1.paired
        83.5%
        52%
        237 bp
        0.5
        S127_R2.paired
        70.0%
        51%
        236 bp
        0.5
        S128_R1.paired
        86.2%
        53%
        243 bp
        0.2
        S128_R2.paired
        71.8%
        51%
        235 bp
        0.2
        S129_R1.paired
        73.8%
        52%
        241 bp
        0.1
        S129_R2.paired
        51.4%
        51%
        231 bp
        0.1
        S130_R1.paired
        78.8%
        53%
        240 bp
        0.4
        S130_R2.paired
        52.5%
        51%
        234 bp
        0.4
        S131_R1.paired
        83.5%
        52%
        242 bp
        0.2
        S131_R2.paired
        64.0%
        51%
        228 bp
        0.2
        S132_R1.paired
        62.1%
        52%
        234 bp
        0.1
        S132_R2.paired
        29.0%
        51%
        231 bp
        0.1
        S133_R1.paired
        82.7%
        52%
        240 bp
        0.2
        S133_R2.paired
        67.3%
        51%
        238 bp
        0.2
        S134_R1.paired
        73.3%
        52%
        244 bp
        0.1
        S134_R2.paired
        51.5%
        50%
        231 bp
        0.1
        S135_R1.paired
        78.2%
        49%
        241 bp
        0.3
        S135_R2.paired
        54.0%
        48%
        236 bp
        0.3
        S136_R1.paired
        76.4%
        52%
        240 bp
        0.1
        S136_R2.paired
        58.7%
        51%
        234 bp
        0.1
        S138_R1.paired
        70.7%
        52%
        242 bp
        0.1
        S138_R2.paired
        32.3%
        51%
        226 bp
        0.1
        S139_R1.paired
        80.8%
        49%
        243 bp
        0.4
        S139_R2.paired
        60.5%
        48%
        236 bp
        0.4
        S13_R1.paired
        84.7%
        52%
        244 bp
        0.2
        S13_R2.paired
        55.8%
        51%
        232 bp
        0.2
        S140_R1.paired
        58.2%
        52%
        241 bp
        0.0
        S140_R2.paired
        23.1%
        51%
        227 bp
        0.0
        S141_R1.paired
        76.9%
        53%
        241 bp
        0.2
        S141_R2.paired
        46.5%
        51%
        222 bp
        0.2
        S142_R1.paired
        60.2%
        52%
        240 bp
        0.0
        S142_R2.paired
        32.3%
        50%
        228 bp
        0.0
        S144_R1.paired
        81.1%
        52%
        240 bp
        0.4
        S144_R2.paired
        54.5%
        51%
        234 bp
        0.4
        S145_R1.paired
        62.0%
        52%
        235 bp
        0.1
        S145_R2.paired
        32.3%
        50%
        235 bp
        0.1
        S14_R1.paired
        85.1%
        52%
        243 bp
        0.2
        S14_R2.paired
        66.8%
        51%
        233 bp
        0.2
        S15_R1.paired
        75.8%
        52%
        240 bp
        0.2
        S15_R2.paired
        50.1%
        51%
        230 bp
        0.2
        S16_R1.paired
        60.3%
        52%
        241 bp
        0.0
        S16_R2.paired
        27.4%
        50%
        235 bp
        0.0
        S17_R1.paired
        82.0%
        54%
        242 bp
        0.2
        S17_R2.paired
        54.2%
        52%
        230 bp
        0.2
        S18_R1.paired
        66.7%
        52%
        235 bp
        0.1
        S18_R2.paired
        41.9%
        51%
        215 bp
        0.1
        S19_R1.paired
        80.4%
        52%
        244 bp
        0.2
        S19_R2.paired
        51.9%
        51%
        234 bp
        0.2
        S1_R1.paired
        71.3%
        52%
        241 bp
        0.1
        S1_R2.paired
        48.9%
        51%
        215 bp
        0.1
        S20_R1.paired
        67.1%
        52%
        242 bp
        0.1
        S20_R2.paired
        40.8%
        51%
        226 bp
        0.1
        S21_R1.paired
        57.4%
        52%
        242 bp
        0.0
        S21_R2.paired
        21.5%
        51%
        227 bp
        0.0
        S22_R1.paired
        46.8%
        50%
        231 bp
        0.1
        S22_R2.paired
        15.4%
        48%
        212 bp
        0.1
        S23_R1.paired
        82.5%
        52%
        243 bp
        0.1
        S23_R2.paired
        68.1%
        51%
        232 bp
        0.1
        S24_R1.paired
        78.7%
        52%
        243 bp
        0.1
        S24_R2.paired
        52.2%
        51%
        225 bp
        0.1
        S25_R1.paired
        75.3%
        52%
        242 bp
        0.1
        S25_R2.paired
        42.5%
        51%
        232 bp
        0.1
        S27_R1.paired
        73.5%
        52%
        241 bp
        0.1
        S27_R2.paired
        47.9%
        51%
        219 bp
        0.1
        S29_R1.paired
        69.4%
        52%
        245 bp
        0.1
        S29_R2.paired
        48.0%
        51%
        231 bp
        0.1
        S2_R1.paired
        77.9%
        52%
        240 bp
        0.3
        S2_R2.paired
        48.7%
        51%
        222 bp
        0.3
        S31_R1.paired
        77.7%
        51%
        245 bp
        0.1
        S31_R2.paired
        41.1%
        50%
        233 bp
        0.1
        S32_R1.paired
        77.1%
        52%
        241 bp
        0.2
        S32_R2.paired
        61.0%
        51%
        223 bp
        0.2
        S33_R1.paired
        62.0%
        52%
        245 bp
        0.0
        S33_R2.paired
        35.8%
        51%
        234 bp
        0.0
        S34_R1.paired
        84.3%
        51%
        244 bp
        0.2
        S34_R2.paired
        54.5%
        50%
        225 bp
        0.2
        S36_R1.paired
        81.6%
        51%
        245 bp
        0.1
        S36_R2.paired
        46.9%
        50%
        235 bp
        0.1
        S38_R1.paired
        76.4%
        52%
        238 bp
        0.1
        S38_R2.paired
        51.0%
        51%
        216 bp
        0.1
        S39_R1.paired
        72.3%
        52%
        240 bp
        0.1
        S39_R2.paired
        51.9%
        50%
        226 bp
        0.1
        S3_R1.paired
        71.8%
        52%
        239 bp
        0.0
        S3_R2.paired
        38.3%
        51%
        232 bp
        0.0
        S40_R1.paired
        67.2%
        52%
        241 bp
        0.1
        S40_R2.paired
        40.6%
        50%
        224 bp
        0.1
        S41_R1.paired
        68.2%
        52%
        242 bp
        0.1
        S41_R2.paired
        47.7%
        51%
        221 bp
        0.1
        S42_R1.paired
        82.3%
        53%
        243 bp
        0.2
        S42_R2.paired
        48.2%
        52%
        231 bp
        0.2
        S43_R1.paired
        72.5%
        52%
        245 bp
        0.0
        S43_R2.paired
        37.1%
        51%
        235 bp
        0.0
        S44_R1.paired
        71.0%
        52%
        240 bp
        0.1
        S44_R2.paired
        38.8%
        51%
        222 bp
        0.1
        S46_R1.paired
        63.9%
        53%
        240 bp
        0.1
        S46_R2.paired
        41.1%
        51%
        224 bp
        0.1
        S47_R1.paired
        79.2%
        52%
        244 bp
        0.2
        S47_R2.paired
        44.2%
        51%
        233 bp
        0.2
        S48_R1.paired
        71.4%
        52%
        227 bp
        0.0
        S48_R2.paired
        40.5%
        51%
        230 bp
        0.0
        S49_R1.paired
        69.9%
        52%
        241 bp
        0.1
        S49_R2.paired
        49.4%
        51%
        225 bp
        0.1
        S51_R1.paired
        75.3%
        52%
        242 bp
        0.1
        S51_R2.paired
        49.0%
        51%
        222 bp
        0.1
        S52_R1.paired
        71.6%
        52%
        240 bp
        0.0
        S52_R2.paired
        26.1%
        51%
        227 bp
        0.0
        S54_R1.paired
        78.4%
        51%
        245 bp
        0.2
        S54_R2.paired
        46.5%
        50%
        230 bp
        0.2
        S55_R1.paired
        77.5%
        53%
        241 bp
        0.2
        S55_R2.paired
        54.6%
        52%
        225 bp
        0.2
        S56_R1.paired
        77.1%
        52%
        241 bp
        0.1
        S56_R2.paired
        61.2%
        51%
        225 bp
        0.1
        S57_R1.paired
        81.4%
        55%
        241 bp
        0.2
        S57_R2.paired
        60.4%
        54%
        217 bp
        0.2
        S58_R1.paired
        72.5%
        53%
        243 bp
        0.1
        S58_R2.paired
        35.2%
        52%
        229 bp
        0.1
        S59_R1.paired
        82.0%
        52%
        245 bp
        0.2
        S59_R2.paired
        49.8%
        51%
        232 bp
        0.2
        S5_R1.paired
        75.1%
        53%
        241 bp
        0.1
        S5_R2.paired
        35.3%
        52%
        223 bp
        0.1
        S60_R1.paired
        75.5%
        51%
        242 bp
        0.1
        S60_R2.paired
        38.0%
        50%
        224 bp
        0.1
        S61_R1.paired
        81.8%
        53%
        242 bp
        0.2
        S61_R2.paired
        55.1%
        52%
        233 bp
        0.2
        S62_R1.paired
        82.3%
        53%
        240 bp
        0.2
        S62_R2.paired
        53.9%
        52%
        231 bp
        0.2
        S63_R1.paired
        76.5%
        53%
        243 bp
        0.1
        S63_R2.paired
        48.7%
        51%
        231 bp
        0.1
        S64_R1.paired
        73.8%
        51%
        237 bp
        0.1
        S64_R2.paired
        46.6%
        50%
        239 bp
        0.1
        S65_R1.paired
        81.7%
        54%
        238 bp
        0.2
        S65_R2.paired
        59.4%
        52%
        234 bp
        0.2
        S66_R1.paired
        48.7%
        52%
        231 bp
        0.1
        S66_R2.paired
        16.6%
        50%
        225 bp
        0.1
        S67_R1.paired
        83.4%
        52%
        241 bp
        0.2
        S67_R2.paired
        71.2%
        51%
        234 bp
        0.2
        S68_R1.paired
        64.6%
        52%
        243 bp
        0.1
        S68_R2.paired
        27.2%
        51%
        233 bp
        0.1
        S69_R1.paired
        75.7%
        50%
        241 bp
        0.2
        S69_R2.paired
        45.2%
        49%
        229 bp
        0.2
        S6_R1.paired
        80.9%
        51%
        245 bp
        0.2
        S6_R2.paired
        45.9%
        50%
        233 bp
        0.2
        S70_R1.paired
        70.3%
        53%
        238 bp
        0.2
        S70_R2.paired
        41.2%
        52%
        236 bp
        0.2
        S71_R1.paired
        69.1%
        52%
        239 bp
        0.2
        S71_R2.paired
        32.1%
        51%
        228 bp
        0.2
        S72_R1.paired
        55.4%
        53%
        234 bp
        0.1
        S72_R2.paired
        31.3%
        52%
        230 bp
        0.1
        S73_R1.paired
        62.5%
        52%
        240 bp
        0.1
        S73_R2.paired
        33.8%
        51%
        238 bp
        0.1
        S74_R1.paired
        72.9%
        53%
        239 bp
        0.1
        S74_R2.paired
        48.5%
        51%
        231 bp
        0.1
        S75_R1.paired
        74.1%
        53%
        241 bp
        0.2
        S75_R2.paired
        54.2%
        51%
        234 bp
        0.2
        S76_R1.paired
        46.0%
        52%
        229 bp
        0.0
        S76_R2.paired
        23.4%
        51%
        225 bp
        0.0
        S77_R1.paired
        70.9%
        52%
        241 bp
        0.1
        S77_R2.paired
        44.0%
        51%
        226 bp
        0.1
        S78_R1.paired
        72.6%
        52%
        239 bp
        0.2
        S78_R2.paired
        48.1%
        51%
        227 bp
        0.2
        S79_R1.paired
        64.9%
        51%
        234 bp
        0.1
        S79_R2.paired
        38.2%
        50%
        237 bp
        0.1
        S7_R1.paired
        66.3%
        52%
        234 bp
        0.1
        S7_R2.paired
        40.1%
        51%
        226 bp
        0.1
        S80_R1.paired
        58.5%
        51%
        236 bp
        0.0
        S80_R2.paired
        14.1%
        49%
        200 bp
        0.0
        S81_R1.paired
        37.1%
        51%
        225 bp
        0.0
        S81_R2.paired
        15.9%
        50%
        211 bp
        0.0
        S82_R1.paired
        79.4%
        53%
        241 bp
        0.3
        S82_R2.paired
        46.8%
        51%
        233 bp
        0.3
        S83_R1.paired
        82.2%
        52%
        245 bp
        0.2
        S83_R2.paired
        56.4%
        51%
        232 bp
        0.2
        S84_R1.paired
        84.4%
        52%
        243 bp
        0.3
        S84_R2.paired
        74.5%
        51%
        239 bp
        0.3
        S85_R1.paired
        75.1%
        54%
        235 bp
        0.3
        S85_R2.paired
        44.2%
        53%
        225 bp
        0.3
        S86_R1.paired
        54.0%
        52%
        238 bp
        0.1
        S86_R2.paired
        19.1%
        50%
        222 bp
        0.1
        S87_R1.paired
        82.2%
        53%
        242 bp
        0.2
        S87_R2.paired
        68.7%
        51%
        234 bp
        0.2
        S89_R1.paired
        68.6%
        52%
        240 bp
        0.2
        S89_R2.paired
        40.5%
        50%
        234 bp
        0.2
        S8_R1.paired
        78.6%
        52%
        226 bp
        0.1
        S8_R2.paired
        58.8%
        51%
        222 bp
        0.1
        S90_R1.paired
        65.5%
        52%
        223 bp
        0.1
        S90_R2.paired
        41.7%
        50%
        228 bp
        0.1
        S91_R1.paired
        78.1%
        50%
        243 bp
        0.2
        S91_R2.paired
        48.8%
        49%
        232 bp
        0.2
        S92_R1.paired
        64.5%
        52%
        233 bp
        0.1
        S92_R2.paired
        43.4%
        51%
        229 bp
        0.1
        S93_R1.paired
        77.3%
        52%
        241 bp
        0.2
        S93_R2.paired
        56.2%
        51%
        238 bp
        0.2
        S94_R1.paired
        64.1%
        54%
        232 bp
        0.1
        S94_R2.paired
        37.2%
        52%
        229 bp
        0.1
        S95_R1.paired
        58.8%
        52%
        219 bp
        0.0
        S95_R2.paired
        28.0%
        50%
        233 bp
        0.0
        S96_R1.paired
        80.0%
        52%
        239 bp
        0.2
        S96_R2.paired
        54.3%
        51%
        236 bp
        0.2
        S97_R1.paired
        87.2%
        53%
        243 bp
        0.3
        S97_R2.paired
        70.5%
        51%
        237 bp
        0.3
        S98_R1.paired
        84.3%
        53%
        238 bp
        0.4
        S98_R2.paired
        62.6%
        52%
        233 bp
        0.4
        S99_R1.paired
        77.4%
        54%
        239 bp
        0.2
        S99_R2.paired
        46.1%
        52%
        234 bp
        0.2
        S9_R1.paired
        87.0%
        53%
        247 bp
        0.1
        S9_R2.paired
        61.5%
        51%
        235 bp
        0.1

        FastQC

        FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.

        Sequence Counts

        Sequence counts for each sample. Duplicate read counts are an estimate only.

        This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

        You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Quality Histograms

        The mean quality value across each base position in the read.

        To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

        Taken from the FastQC help:

        The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Sequence Quality Scores

        The number of reads with average quality scores. Shows if a subset of reads has poor quality.

        From the FastQC help:

        The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called.

        To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        From the FastQC help:

        Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

        In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

        It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

        Click a sample row to see a line plot for that dataset.
        Rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

        From the FastQC help:

        This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

        In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

        An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Base N Content

        The percentage of base calls at each position for which an N was called.

        From the FastQC help:

        If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Length Distribution

        The distribution of fragment sizes (read lengths) found. See the FastQC help

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Duplication Levels

        The relative level of duplication found for every sequence.

        From the FastQC Help:

        In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (eg PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Overrepresented sequences

        The total amount of overrepresented sequences found in each library.

        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as over represented.

        Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

        From the FastQC Help:

        A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

        FastQC lists all of the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Adapter Content

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

        Note that only samples with ≥ 0.1% adapter contamination are shown.

        There may be several lines per sample, as one is shown for each adapter detected in the file.

        From the FastQC Help:

        The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Status Checks

        Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        FastQC assigns a status for each section of the report. These give a quick evaluation of whether the results of the analysis seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        It is important to stress that although the analysis results appear to give a pass/fail result, these evaluations must be taken in the context of what you expect from your library. A 'normal' sample as far as FastQC is concerned is random and diverse. Some experiments may be expected to produce libraries which are biased in particular ways. You should treat the summary evaluations therefore as pointers to where you should concentrate your attention and understand why your library may not look random and diverse.

        Specific guidance on how to interpret the output of each module can be found in the relevant report section, or in the FastQC help.

        In this heatmap, we summarise all of these into a single heatmap for a quick overview. Note that not all FastQC sections have plots in MultiQC reports, but all status checks are shown in this heatmap.

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